Birth, Bacteria, and Biology

We’re all probably pretty familiar with microbes in one way or another, whether we realize it or not. Our microbial makeup is essential to health and well-being, and we each begin a symbiotic relationship with these good bacteria at the moment of birth. Prior to entering this world, it is assumed that the developing fetus exists in a relatively sterile environment within the womb. However, “the moment we enter the world, microbes colonize our bodies. And depending on how and where we’re born, we’re colonized by different types of microbes,” according to the Genetic Science Learning Center of the University of Utah. This colonization begins in the birth canal, where a baby is first coated with a film of microbes.


However, not all babies are born vaginally, and those that are taken by cesarian section are exposed to an entirely different set of microbes that exist on the mother’s skin. So, when the natural process of childbirth is disrupted in such a way, the beneficial bacteria that are supposed to help a baby transition into a new bacteria filled environment can’t coat the baby and they won’t get all the good microbes they should. And research is showing that there are long-ranging benefits for babies exposed to the microbes that exist in their mothers’ vaginas. A 2015 article on the subject that was published in the Guardian speaks to the lifelong impact these microbes make:

“What’s more, the difference in the microbiome resulting from the mode of delivery persists over time. Caesarean-born infants have a more slowly diversifying microbiota, even after six months of age – and a 2014 Dutch study found these differences still existed in children at seven years of age.

‘What we’re finding is that interaction with microbes very early on in life will lead to a certain immune pathway – a tolerizing one or one that is more disease producing,’ says Dr Josef Neu, a professor of pediatrics at the University of Florida.”


Medical science is now beginning to recognize the importance of the microbiome, and also the microbial coating effect that occurs in the birth canal. Mothers who are looking toward delivering their babies by c-section are now making efforts to mimic this phenomenon through a process called “vaginal seeding.” This basically involves placing a piece of gauze soaked in saline solution into the vagina, and then setting that aside in a sealed container until the baby is surgically removed. As soon as the baby is out, it’s mouth, eyes, and skin are swabbed with the gauze, effectively introducing the microbes that the baby would have encountered if it came through the birth canal.


While this doesn’t give a newborn full exposure to the microbes they need, it will at least give them an introduction to them. What is really important about the microbes a baby encounters while passing through the vagina is that they help to establish the immune system and set up a healthy gut environment so the child can thrive outside the womb. An article in the Journal of Pediatric Gastroenterology and Nutrition gives a good characterization of the process of the establishment of this “pioneer microbiome” in infants:

“These initial colonizing species have come to be recognized as a pioneer microbiome, one that educates the developing immune system and provides favorable conditions for colonization by subsequent microbes, through production of an anaerobic environment, favorable substrates for bacterial growth, and protection from the systemic immune system (4). This pioneer microbiome also has lifelong implications: bacterial strains sampled from adults are often shared between siblings and parents, demonstrating that childhood colonization can persist throughout adulthood (8).”


These microbes also serve to help newborns digest their first meal, which is always best when coming from the mother in the form of breast milk. It is well established that breastfed babies are less susceptible to illness than their formula-fed counterparts, and the reason for this is that antibodies are passed from the mother’s milk directly to the infant’s intestine. These interactions between the antibodies from breast milk and the microbes transmitted through vaginal secretions are what help to establish and maintain a human’s gut microbiome. And a healthy gut can be the main deciding factor between having a lifetime of wellness and vitality, or one of sickness and disease.


The beneficial organisms we are exposed to at birth continue to help us build immunities and digest food throughout our entire lives. It is best to get optimum exposure by travelling through the birth canal and being birthed vaginally, but if this isn’t possible, even a Cesarean born baby can have these microbes introduced through vaginal seeding. The early establishment of a healthy gut environment has far reaching effects well beyond birth. It truly can be the difference between a long, healthy lifetime or a diminished lifespan marked by illness.

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About Evan Farmer (81 Articles)
Father of four beautiful boys, the first two of which are twins...husband, artist, writer, barista, and a reluctant entrepreneur; my wife Koren and I own Cuppa - Handcrafted Coffee and Espresso Creations, which is located in downtown Jackson, MI. I'm also a freelance writer and WordPress web developer, a bicycle enthusiast and an avid gardener.
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